We rearrange the genetic code and present a table of codons. The chemical properties of the amino acids coded by codons, and the evolutionary trend of codons are well reflected in the order of this table, from which two rules can be drawn: (1) the polarity/non-polarity and hydrophilicity/hydrophobicity of amino acids coded for by codons alternate row by row in the table; (2) in general, the low...

A recommendation of: Brandon Kwee Boon Seah, Aditi Singh, Estienne Carl Swart Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons https://doi.org/10.1101/2022.04.12.488043

Background: Most of the amino acids are encoded by more than one codon, termed as synonymous codons. Synonymous codon usage is not random as it is unique to species. In each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (SCUB). Trends associated with evolution of SCUB and factors influencing its diversification in plastomes of gen...

The X circular code is a set of 20 trinucleotides (codons) that has been identified in the protein-coding genes most organisms (bacteria, archaea, eukaryotes, plasmids, viruses). It shown previously important mathematical property being an error-correcting code. Thus, motifs code, i.e. series codons belonging to and called motifs, allow identification maintenance reading frame genes. are signif...

AGA and AGG codons for arginine are the least used codons in Escherichia coli. Previous findings have shown that these codons are used preferentially within the first 25 codons in E. coli genes. More than 100 genes having a single AGA/AGG codon within the first 25 codons were identified to be associated with various essential cellular functions. The lacZ gene, containing 5 AGG codons after the ...

In eukaryotes, the polypeptide release factor 1 (eRF1) is involved in translation termination at all three stop codons. However, the mechanism for decoding stop codons remains unknown. A direct interaction of eRF1 with the stop codons has been postulated. Recent studies focus on eRF1 from ciliates in which some stop codons are reassigned to sense codons. Using an in vitro assay based on mammali...

background: most of the amino acids are encoded by more than one codon, termed as synonymous codons. synonymous codon usage is not random as it is unique to species. in each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (scub). trends associated with evolution of scub and factors influencing its diversification in plastomes of gen...

Our understanding of translation underpins our capacity to engineer living systems. The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are considered as the 'start codons' for translation initiation in Escherichia coli. Translation is typically not thought to initiate from the 61 remaining codons. Here, we quantified translation initiation of green fluorescent protein and nanolu...